<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
<html> <head>
<title>Generic Genome Browser</title>
<link rel="stylesheet" href="tutorial/tutorial.css">
</head>

<body>
<h1>Generic Genome Browser, v2</h1>

<a href="http://www.gmod.org/"><img src="gmod_cog.jpeg" border="0" align="RIGHT"></a>

<p>

Welcome to the Generic Genome Browser!

<h2>Documentation</h2>

<dl>
  <dt><b>Online tutorial and sample data files</b></dt>
  <dd><a href="tutorial/tutorial.html">/var/www/gbrowse2/tutorial<a>.</dd>
  <dt><b>Installation and configuration manual</b></dt>
  <dd><a href="http://gmod.org/wiki/GBrowse_2.0_HOWTO">GBrowse 2.0 HOWTO</a></dd>
  <dt><b>Example scripts to control GBrowse from the command line</b></dt>
  <dd><a href="example_scripts">/var/www/gbrowse2/example_scripts</a></dd>
</dl>

<h2>Example Databases</h2>

<p>

Example in-memory databases from yeast chromosomes 1 and 2 have been
installed for you.  Try them at these URL:

<ul>
<li><a href="/cgi-bin/gb2/gbrowse/yeast">http://your.host/cgi-bin/gb2/gbrowse/yeast</a> (simple example)</li>
<li><a href="/cgi-bin/gb2/gbrowse/yeast_advanced">http://your.host/cgi-bin/gb2/gbrowse/yeast_advanced</a> (advanced example)</li>
<li><a href="/cgi-bin/gb2/gbrowse/yeast_renderfarm">http://your.host/cgi-bin/gb2/gbrowse/yeast_renderfarm</a> (yeast_renderfarm example)</li>
</ul>

<p>
The "yeast_renderfarm" example will only work if a local gbrowse_slave
render slave daemon is running. To launch the daemon, run this command
as the root user:

<pre>
% /etc/init.d/gbrowse-slave start
</pre>

<h3>Alternative URLs</h3>

If you allowed the install process to adjust your Apache
configuration, you can use the alias /gb2 as an alternative to
/cgi-bin/gb2:

<ul>
<li><a href="/gb2/gbrowse/yeast">http://your.host/gb2/gbrowse/yeast</a></li>
<li><a href="/gb2/gbrowse/yeast_advanced">http://your.host/gb2/gbrowse/yeast_advanced</a></li>
<li><a href="/gb2/gbrowse/yeast_renderfarm">http://your.host/gb2/gbrowse/yeast_renderfarm</a></li>
<li><a href="/gb2/gbrowse/pop_demo">http://your.host/gb2/gbrowse/pop_demo</a> (demo of embedded population allele frequency maps -- requires Template module to be installed)</li>
</ul>

<h3>Accelerated Demos</h3>

If you have mod_fcgid, mod_fastcgi and/or ModPerl installed, you will have access to
an accelerated version of gbrowse at these URLs:

<ul>
  <li>mod_fcgid
      <ul>
	<li><a href="/fgb2/gbrowse/yeast">http://your.host/fgb2/gbrowse/yeast</a></li>
	<li><a href="/fgb2/gbrowse/yeast_advanced">http://your.host/fgb2/gbrowse/yeast_advanced</a></li>
	<li><a href="/fgb2/gbrowse/yeast_renderfarm">http://your.host/fgb2/gbrowse/yeast_renderfarm</a></li>
      </ul>
  </li>
  <li>mod_fastcgi
      <ul>
	<li><a href="/fast/gbrowse/yeast">http://your.host/fast/gbrowse/yeast</a></li>
	<li><a href="/fast/gbrowse/yeast_advanced">http://your.host/fast/gbrowse/yeast_advanced</a></li>
	<li><a href="/fast/gbrowse/yeast_renderfarm">http://your.host/fast/gbrowse/yeast_renderfarm</a></li>
      </ul>
  </li>
  <li>mod_perl
      <ul>
	<li><a href="/mgb2/gbrowse/yeast">http://your.host/mgb2/gbrowse/yeast</a></li>
	<li><a href="/mgb2/gbrowse/yeast_advanced">http://your.host/mgb2/gbrowse/yeast_advanced</a></li>
	<li><a href="/mgb2/gbrowse/yeast_renderfarm">http://your.host/mgb2/gbrowse/yeast_renderfarm</a></li>
      </ul>
  </li>
</ul>


<h2>Directory Paths</h2>

<p>

For future reference, here is where you've installed GBrowse's various
components:

<dl>
  <dt>GBrowse documentation, stylesheets and in-memory databases.
  <dd><b>$HTDOCS</b>
      <p>
  <dt>GBrowse configuration files
  <dd><b>$CONF</b>
      <p>
  <dt>Preinstalled sample database(s)
  <dd><b>$DATABASES</b>
      <p>
  <dt>GBrowse CGI (web) scripts
  <dd><ul>
          <li><b>$CGIBIN/gbrowse</b>
          <li><b>$CGIBIN/gbrowse_img</b>
          <li><b>$CGIBIN/gbrowse_details</b>
      </ul>
      <p>
  <dt>Temporary directories for cached images and sessions.
  <dd><b>$TMP</b>
</dl>

<p>

<h2>Learning More</h2>

<p>

To find out more about Gbrowse, try the:

<ul>
  <li><a href="http://gmod.org/wiki/GBrowse_2.0_HOWTO">GBrowse 2.0 HOWTO</a>
  <li><a href="tutorial/tutorial.html">GBrowse Tutorial</a>
 <!-- <li><a href="contrib/conf_files">Sample Configuration Files</a> -->
</ul>


<hr>
<address>Lincoln D. Stein, lstein@cshl.org<br>
<a href="http://www.cshl.org/">Cold Spring Harbor Laboratory</a></address>
<!-- hhmts start -->
Last modified: Thu Mar 18 18:59:16 PDT 2010
<!-- hhmts end -->
</body> </html>
